Mach3 / Offsets / Tool setup etc

I am running Mach3, and using "Emachine shop" as CAD and CAMBAM as my CAM software.

I have this controller ; http://www.easy-cnc.com/web/download...s%28NEW%29.pdf

1/ Is there an easy way to set one of these toolsetters up : DamenCNC.com - DCNC-ToolSetter with Mach3 ?

2/ I find offsets quite confusing, although I have gotten my head around it. (I think)
My controller manual states I cannot use the limit switches connected 'to it and the x,y and Z axis', for home switches. Is there a way I can connect the switches directly to the LPT1 port to utilize them as home switches without damaging the controller ?